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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        About MultiQC

        This report was generated using MultiQC, version 1.31

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-09-15, 18:34 IST based on data in: /Volumes/Crucial X6/wgs_analysis_hackbio/kraken_results

        General Statistics

        Showing 26/26 rows and 3/3 columns.
        Sample NameListeria monocytogenesTop 5 speciesUnclassified
        SRR27013311_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        74.2%
        75.6%
        12.0%
        SRR27013312_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        74.1%
        75.9%
        12.9%
        SRR27013313_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        65.2%
        65.9%
        25.8%
        SRR27013314_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        59.3%
        60.4%
        20.4%
        SRR27013315_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        78.6%
        83.0%
        9.8%
        SRR27013316_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        71.3%
        77.9%
        5.9%
        SRR27013325_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        77.2%
        78.9%
        13.0%
        SRR27013326_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        72.9%
        76.3%
        11.9%
        SRR27013327_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        66.3%
        69.8%
        14.6%
        SRR27013328_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        74.3%
        77.6%
        15.8%
        SRR27013329_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        78.0%
        83.0%
        7.7%
        SRR27013330_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        73.0%
        77.9%
        11.3%
        SRR27013331_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        76.5%
        80.8%
        12.2%
        SRR27013332_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        70.8%
        78.8%
        11.4%
        SRR27013333_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        70.9%
        74.1%
        14.2%
        SRR27013334_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        79.5%
        80.2%
        11.6%
        SRR27013335_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        79.3%
        81.3%
        10.8%
        SRR27013336_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        78.1%
        80.3%
        5.5%
        SRR27013337_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        10.5%
        89.7%
        4.7%
        SRR27013337_report
        10.5%
        89.7%
        4.7%
        SRR27013338_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        66.0%
        80.7%
        8.0%
        SRR27013339_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        64.3%
        74.5%
        16.4%
        SRR27013340_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        54.1%
        61.3%
        10.8%
        SRR27013341_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        64.4%
        66.2%
        19.9%
        SRR27013342_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        56.4%
        61.3%
        15.1%
        SRR27013343_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs_report
        59.9%
        62.7%
        19.2%

        Kraken

        Taxonomic classification using exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.URL: https://ccb.jhu.edu/software/krakenDOI: 10.1186/gb-2014-15-3-r46

        Top taxa

        The number of reads falling into the top 5 taxa across different ranks.

        To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 5 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.

        The total number of reads is approximated by dividing the number of unclassified reads by the percentage of the library that they account for. Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.

        The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.

        Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.

        Created with MultiQC